 
 (defn -run
   ([this acq-settings cleanup? position-list autofocus-device]
-    (let [settings (convert-settings acq-settings)]
+    (let [settings (convert-settings acq-settings position-list)]
       (run this settings cleanup? position-list autofocus-device)))
   ([this acq-settings cleanup?]
-    (let [settings (convert-settings acq-settings)]
-      (run this settings cleanup? (.getPositionList gui) (.. gui getAutofocusManager getDevice))))
+    (let [position-list (.getPositionList gui)
+          settings (convert-settings acq-settings position-list)]
+      (run this settings cleanup? position-list (.. gui getAutofocusManager getDevice))))
   ([this acq-settings]
     (-run this acq-settings true)))
 

                                         ProcessorStack SequenceSettings
                                         MMAcquisition
                                         TaggedImageStorageRam]
           [org.micromanager.utils ReportingUtils]
           [mmcorej TaggedImage Configuration Metadata]
           (java.util.concurrent Executors TimeUnit)

            (assoc :frames (range (.numFrames settings))
                   :channels (vec (filter :use-channel
                                          (map ChannelSpec-to-map (.channels settings))))
                   :positions (vec (range (.getNumberOfPositions position-list)))
                   :slices (vec (.slices settings))
                   :default-exposure (core getExposure)
                   :custom-intervals-ms (vec (.customIntervalsMs settings)))
